4OAV | pdb_00004oav

Complete human RNase L in complex with 2-5A (5'-ppp heptamer), AMPPCP and RNA substrate.

PDB DOI: https://doi.org/10.2210/pdb4OAV/pdb
NAKB: 4OAV

Classification: HYDROLASE/RNA
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-01-06 Released: 2014-03-12
Deposition Author(s): Han, Y., Donovan, J., Rath, S., Whitney, G., Chitrakar, A., Korennykh, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.229 (Depositor), 0.232 (DCC)
R-Value Work:
0.198 (Depositor), 0.201 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure of human RNase L reveals the basis for regulated RNA decay in the IFN response.

Han, Y., Donovan, J., Rath, S., Whitney, G., Chitrakar, A., Korennykh, A.

(2014) Science 343: 1244-1248

PubMed: 24578532 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.1249845
Primary Citation Related Structures:
4OAU, 4OAV

PubMed Abstract:
One of the hallmark mechanisms activated by type I interferons (IFNs) in human tissues involves cleavage of intracellular RNA by the kinase homology endoribonuclease RNase L. We report 2.8 and 2.1 angstrom crystal structures of human RNase L in complexes with synthetic and natural ligands and a fragment of an RNA substrate. RNase L forms a crossed homodimer stabilized by ankyrin (ANK) and kinase homology (KH) domains, which positions two kinase extension nuclease (KEN) domains for asymmetric RNA recognition. One KEN protomer recognizes an identity nucleotide (U), whereas the other protomer cleaves RNA between nucleotides +1 and +2. The coordinated action of the ANK, KH, and KEN domains thereby provides regulated, sequence-specific cleavage of viral and host RNA targets by RNase L.

Organizational Affiliation

Department of Molecular Biology, Princeton University, 216 Schultz Laboratory, Princeton, NJ 08540, USA.

Macromolecule Content

Total Structure Weight: 163.47 kDa
Atom Count: 11,963
Modeled Residue Count: 1,361
Deposited Residue Count: 1,412
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (RNase L)	A [auth B], C [auth D]	699	Homo sapiens	Mutation(s): 1 EC: 3.1.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q05823 (Homo sapiens) Explore Q05823 Go to UniProtKB: Q05823
PHAROS: Q05823 GTEx: ENSG00000135828
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q05823
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
RNA (5'-R(P(PO4)P(PO4)PAPAPAPAP*(PO4))-2')	B [auth A], D [auth C]	7	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PUP Query on PUP Download:Ideal Coordinates CCD File SDF format, chain K [auth D] MOL2 format, chain K [auth D] mmCIF format, chain K [auth D]	K [auth D]	(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-4-hydroxy-2-({[(S)-hydroxy{[(2R,3S,4S)-4-hydroxy-2-(hydroxymethyl)tetrahydrofuran-3-yl]oxy}phosphoryl]oxy}methyl)tetrahydrofuran-3-yl dihydrogen phosphate C₁₄ H₂₂ N₂ O₁₅ P₂ CTEYAHSJKMGMOL-HHUJUQMJSA-N		Interactions Focus chain K [auth D] Interactions & Density Focus chain K [auth D]
ACP Query on ACP Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain E [auth B] MOL2 format, chain H [auth D] MOL2 format, chain E [auth B] mmCIF format, chain H [auth D] mmCIF format, chain E [auth B]	E [auth B], H [auth D]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain E [auth B] Focus chain H [auth D] Interactions & Density Focus chain E [auth B] Focus chain H [auth D]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain I [auth D] SDF format, chain G [auth B] SDF format, chain F [auth B] MOL2 format, chain J [auth D] MOL2 format, chain I [auth D] MOL2 format, chain G [auth B] MOL2 format, chain F [auth B] mmCIF format, chain J [auth D] mmCIF format, chain I [auth D] mmCIF format, chain G [auth B] mmCIF format, chain F [auth B]	F [auth B], G [auth B], I [auth D], J [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth D] Focus chain J [auth D] Interactions & Density Focus chain F [auth B] Focus chain G [auth B] Focus chain I [auth D] Focus chain J [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.229 (Depositor), 0.232 (DCC)
R-Value Work: 0.198 (Depositor), 0.201 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.61	α = 90
b = 160.7	β = 90
c = 230.8	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHENIX	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-03-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-03-12
Type: Initial release
Version 1.1: 2014-04-02
Changes: Database references
Version 1.2: 2023-09-20
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description